Curriculum

The Office of Graduate Affairs (OGA) hosts a number of lectures/mini-courses on Experimental Design, Reesrach and Date Integrity, Laboratory Safety, Title IV Training and Student Conduct, including sexual harrassment and sexual violence prevention and responses.  OGA and the Graduate Student Organization (GSO) also hold a series of orientation events to acclimatize first-year students to the CUIMC campus and to NYC.  

The Program Directors and Coordinator interact with trainees in the summer prior to matriculation to help them get acquainted with the program, and to make sure that they have been able to make housing arrangements. The Program Directors meet virtually with incoming students during the summer to discuss possible mentors for their first rotation. Faculty are asked prior to these meetings whether they are willing/able to host a rotation student. At orientation, Program Directors meet with students to discuss the basics of the program, including course requirements, laboratory rotations, qualifying examinations and student seminars, and to answer any questions students may have. The Program Directors are responsible for advising first-year students regarding coursework, rotations and other issues that arise. They meet individually with the first-year students three times a year, once at orientation (in the beginning of the school year) and at the end of each semester. 

To create an equitable and inclusive method for students and potential mentors to meet one another, we created a faculty poster session. This poster session is open to all faculty on campus and is held during orientation week for new PhD students. Faculty are not allowed to send delegates in their place.

The most important information that students must have for rotation selection is the faculty research interests. As noted in Orientation session, there is a Faculty Poster Session during orientation that allows new students to learn more about the research at Columbia VP&S. Each faculty member also has a research description on the program website, but given the large number of faculty and areas of research that students can choose from, individual orientation interviews with the program directors are very important to help guide students to appropriate laboratories. Students are required to do at least two rotations, but they generally complete three rotations during their first year. The first rotation typically begins in September and lasts until winter break (~3rd week in December), the second rotation spans January-March and the third rotation is from April-June. Occasionally it is necessary for a student to do a fourth rotation, although this is not encouraged.   

The Program Coordinator obtains written rotation evaluations from faculty mentors at the end of the rotation period. The Program Directors discuss these reports with trainees during their regularly scheduled meetings at the end of each semester. In the event that trainees are having difficulties with rotations, the Program Directors will meet separately with trainees and rotation mentors to discuss problems that arose and how they can be addressed.

After the third rotation, students should choose a thesis laboratory in consultation with the Program Directors and their chosen mentors.

• First year fall semester: Biochemistry, Cell and Molecular Biology I, Molecular Genetics
• First year spring semester: Biochemistry, Cell and Molecular Biology II, Statistics for the Basic Sciences, Elective
• Second year fall semester: Elective
• Second year spring semester: Responsible Conduct of Research and Related Policy Issues,
• Third year fall semester: Small Group Discussion - Responsible Conduct of Research

During the second semester of their second year, students prepare for their qualifying examinations. This examination is used as a formal evaluation of the student’s potential as a candidate for the Ph.D. degree. It is designed to assess the student’s ability to develop a sophisticated, in-depth understanding of their thesis project and also to serve as a tool for identifying deficiencies in the student’s background that could be remedied by further coursework and/or additional reading.   

Students present a written research proposal on their thesis topic.  The proposal is written in the format of an NIH F31 fellowship, consisting of a description of the background and significance of the topic, specific aims, and research approach to address the aims. Preliminary data can also be presented if available, but given that the examination occurs shortly after trainees begin their projects, it is not required. Students along with their thesis advisors propose three possible committee members who will serve as examiners. The Program Directors review the proposed committee members and, if they approve, a qualifying examination is scheduled by the student. Proposals are submitted to the committee one week prior to the examination, and a committee chair is chosen by the Program Directors.  At the qualifying examination, students present a ‘chalk talk’ of their proposal and are examined on the proposal, as well as other topics relevant to the project or covered in the students’ coursework.

6-9 months after the qualifying examination, students are expected to have their first thesis committee meeting. The thesis committee composition is typically the same as the qualifying examination committee, although occasionally one or more of the members might be replaced, particularly if a student’s research is going in a different direction. Thesis committees provide scientific expertise related to students’ research projects and monitor their progress. For the first committee meeting, students present a short written report that contains the Specific Aims of their proposal and any progress they have made since the qualifying examination. The committee discusses with students their progress to date and priorities for the order in which work will proceed, as well as the design of experiments. The committee may recommend changes to experimental design or priorities. The committee also decides when to have the next meeting, which can occur 3, 6 or 9 months after the current meeting. For subsequent thesis committee meetings, students should prepare a 1-2 page report outlining their progress and presenting a timetable for experimental progress and thesis completion. The committee can and should recommend improvements to experimental strategies and fallback plans for difficult or risky projects. 

Guidelines for writing your thesis

Here are some guidelines for the order and content of what should be included in your Dissertation

Chapter 1: Introduction – this should be a scholarly synthesis of the background that forms the foundation for the thesis work. It should be comprehensive (30–40 pages) and have original (primary) references – avoid referencing other reviews. The level of detail should be similar to a review in the Annual Reviews series. 

Chapter 2: Materials and Methods – this section should contain all of the methods for the entire thesis. Even if the student has published a paper, they still should compile all the methods into one chapter. 

Chapters 3, 4, etc.: These chapters comprise results that are typically presented in individual manuscripts – each chapter should have a short (1–3 page) introduction, followed by results and figures (thesis format requires figures and legends on separate pages), and concluding with a short discussion. 

Final chapter: Conclusions and future directions. 

Appendices can include computer codes, tables, and any extra random results you want to put in the thesis but don’t belong to any manuscript.

After the thesis committee gives its approval for a student to write their thesis, the defense is scheduled. The final thesis committee consists of the mentor, the three thesis committee members, and one additional outside examiner. If the additional examiner is from outside the university, s/he has to be approved by the Program and the Dissertation Office as a competent examiner. The thesis should be submitted to the committee two weeks before the scheduled defense. A public presentation is given immediately before the closed defense. At the time of the closed defense, the student may be asked to make additional revisions that will then need to be approved by the mentor and one other member of the committee (assigned at the time of the defense). On rare occasions, the student may be required to do additional experimental work, extensive revisions of the thesis, and a second dissertation defense. Students are required to submit a first author paper before their defense. This paper can be submitted to bioRxiv. 

First and second year students participate in the Student Seminar series in both the fall and spring semesters. This series is held every other Tuesday evening and the overall goals of the Seminar course are to: 

• Learn about cellular & molecular biology, broadly defined 
• Learn about research at Columbia/VP&S 
• Learn about scientists as individuals 
• Learn how to give a research presentation to an educated – but non-expert – audience 
• Learn how to give useful feedback 
• Learn how to work as a team to plan and host a seminar series 

Fall Semester: Fall semester is structured as a ~bi-weekly seminar series, planned the prior Spring by rising second-year students in the Program. Second-year students host ~5-6 faculty speakers that are diverse in terms of research topics, personal identities, and career paths. Faculty speakers are asked to speak for ~20 minutes on their research and ~20 minutes on their career trajectory, with ~20 min for open discussion. 

Spring Semester: Spring semester is structured as a ~bi-weekly series where the speakers are first-year students. During each session, two first-year students will give a ~15 minute talk about one of their rotation projects. It is not the intention to overburden students amidst other coursework. In most cases, students will have given at least one presentation in at least one of their rotations, so they will have at least one slide presentation already prepared for use in this exercise. All students in attendance provide feedback on each presentation by submitting a survey form highlighting the strengths and weaknesses of the presentation. Course directors collect the feedback forms and meet with each presenter during the following week to discuss their presentation and provide constructive feedback. 

The program has an annual retreat. Every other year it is a 2-day event, overnight at an off-campus venue. On alternate years, it is a 1-day event held on-campus. Two senior PhD students and two junior faculty are selected to work together to plan the retreat. All presentations are by students.

The goal for this course is to help students navigate the world after the Ph.D.  We will have a series of 11 seminars on careers that our trainees most commonly choose or express interest in. Sessions will feature invited speakers, each with a Ph.D. in biomedical science. Speakers will introduce their experience from their Ph.D. to their current profession followed by questions and discussion.  A reception will follow. The seminar series is open to all PhD students and post-docs in the biomedical sciences.  Students and post-docs can optionally register for the course for credit, or drop in for one or more sessions. The final (optional) session will be a CV workshop for students and postdocs applying for academic positions.

Course Directors: Shan Zha, Ron Liem, Becky Haeusler, and Yinghui Mao.